I'm having the same issue with my Thrustmaster Top Gun Afterburner stick and throttle. I wrote a VB.NET program to test getting the imputs directly and all the numbers are correct. I translated that program to C# and put it in a unity script and it returns 0 (zero) for all impute.

Note: It requires winmm.dll to work and I put a copy of that in the plugins folder.

I think Unity's connections to the windows joystick drivers has a bug in it based on the fact that all other games and programs do not experience this issue with the inputs being screwed up.